you are going to need to make a new desktop file for tor and place it somewhere the menu knows to look. usually /usr/share/applications, but ~/.local/share/applications should work too, and just for the particular user, if that sort of thing is important.

Get the file out of the applications folder, it's not meant to go there. Gnome users can use menulibre to add new additions to the menu... but did you check the Debian wiki for any instructions for the Tor Browser? They suggest using torbrowser-launcher to install it. For now, use the MX package-installer to install it from the Stretch backports repo, that should get it and create a menu entry automatically.